Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001119.1 Hibiscus syriacus cultivar Beakdansim tig00002215_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 78659
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:212 original size:24 final size:24
Alignment explanation
Indices: 180--240 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 24
170 CAGAAGTGAT
*
180 TAAATTTTAAAGAAGATATATG-CA
1 TAAAATTTAAAGAAGATA-ATGACA
* *
204 TAAAATTT-AATAAGTTAATGACA
1 TAAAATTTAAAGAAGATAATGACA
*
227 TAAAATATAAAGAA
1 TAAAATTTAAAGAA
241 ATCAAGTTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 3 0.10
23 16 0.53
24 11 0.37
ACGTcount: A:0.56, C:0.03, G:0.10, T:0.31
Consensus pattern (24 bp):
TAAAATTTAAAGAAGATAATGACA
Found at i:3428 original size:2 final size:2
Alignment explanation
Indices: 3345--3416 Score: 114
Period size: 2 Copynumber: 37.5 Consensus size: 2
3335 GTCACAATCC
3345 AT AT AT AT AT AT AT AT A- AT -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3385 AT AT AT AT AT -T AT AG AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3417 CCTAATATAT
Statistics
Matches: 65, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
1 3 0.05
2 62 0.95
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3546 original size:21 final size:21
Alignment explanation
Indices: 3522--3595 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
3512 AAGGTTAGAA
3522 TTTAAGATTTAGATTTTAAGG
1 TTTAAGATTTAGATTTTAAGG
* *
3543 TTTAAGATAT-GATTTTTAGAG
1 TTTAAGATTTAGATTTTAAG-G
3564 TTT-AGAATTTTAGGA-TTTAAGG
1 TTTAAG-A-TTTA-GATTTTAAGG
*
3586 TTTAGGATTT
1 TTTAAGATTT
3596 GATATTAGAG
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
20 10 0.24
21 17 0.40
22 7 0.17
23 6 0.14
24 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (21 bp):
TTTAAGATTTAGATTTTAAGG
Found at i:4812 original size:30 final size:29
Alignment explanation
Indices: 4776--4832 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
4766 CCGTATTAGG
* *
4776 CACTAAACTTTAACAATGTATCAATTTTGT
1 CACTAAAATTTAAAAATG-ATCAATTTTGT
*
4806 CACTAAAATTTAAAAATGCTCAATTTT
1 CACTAAAATTTAAAAATGATCAATTTT
4833 AGGTATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.39
Consensus pattern (29 bp):
CACTAAAATTTAAAAATGATCAATTTTGT
Found at i:7958 original size:15 final size:15
Alignment explanation
Indices: 7938--7990 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
7928 TATTAGAATT
7938 TTTGAATTACTGAAA
1 TTTGAATTACTGAAA
7953 TTTGAATTACTGAAA
1 TTTGAATTACTGAAA
** * *
7968 AATAAATTACTGGAA
1 TTTGAATTACTGAAA
7983 TTTGAATT
1 TTTGAATT
7991 CTGGAAAATG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.40
Consensus pattern (15 bp):
TTTGAATTACTGAAA
Found at i:7978 original size:30 final size:29
Alignment explanation
Indices: 7942--8005 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 29
7932 AGAATTTTTG
7942 AATTACTGAAATTTGAATTACTGAAAAATA
1 AATTACTGAAATTTGAATT-CTGAAAAATA
* * *
7972 AATTACTGGAATTTGAATTCTGGAAAATG
1 AATTACTGAAATTTGAATTCTGAAAAATA
8001 AATTA
1 AATTA
8006 TATTTTTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 13 0.42
30 18 0.58
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.34
Consensus pattern (29 bp):
AATTACTGAAATTTGAATTCTGAAAAATA
Found at i:8002 original size:14 final size:15
Alignment explanation
Indices: 7940--8005 Score: 64
Period size: 15 Copynumber: 4.5 Consensus size: 15
7930 TTAGAATTTT
*
7940 TGAATTACT-GAAATT
1 TGAATTACTGGAAA-A
*
7955 TGAATTACTGAAAAA
1 TGAATTACTGGAAAA
* **
7970 TAAATTACTGGAATT
1 TGAATTACTGGAAAA
7985 TGAATT-CTGGAAAA
1 TGAATTACTGGAAAA
7999 TGAATTA
1 TGAATTA
8006 TATTTTTTGA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
14 12 0.30
15 25 0.62
16 3 0.08
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAAAA
Found at i:8328 original size:12 final size:12
Alignment explanation
Indices: 8313--8346 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
8303 TTAATTAGTA
8313 TATTTAAATATT
1 TATTTAAATATT
*
8325 TATTAAAATA-T
1 TATTTAAATATT
8336 TATTTAAATAT
1 TATTTAAATAT
8347 ATAATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TATTTAAATATT
Found at i:8335 original size:20 final size:20
Alignment explanation
Indices: 8298--8336 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
8288 TATATTTTAA
**
8298 AAATATTAATTAGTATATTT
1 AAATATTAATTAAAATATTT
*
8318 AAATATTTATTAAAATATT
1 AAATATTAATTAAAATATT
8337 ATTTAAATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
AAATATTAATTAAAATATTT
Found at i:12539 original size:25 final size:25
Alignment explanation
Indices: 12511--12562 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
12501 ATAAATTACT
*
12511 TGTTTAAGTTCTGGTTAACACAAAG
1 TGTTTAAGTTCTGATTAACACAAAG
* *
12536 TGTTTAAGTTCTGATTAATATAAAG
1 TGTTTAAGTTCTGATTAACACAAAG
12561 TG
1 TG
12563 ATAAGCTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (25 bp):
TGTTTAAGTTCTGATTAACACAAAG
Found at i:22300 original size:14 final size:14
Alignment explanation
Indices: 22266--22302 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
22256 AATTATCATT
22266 TTTTTTAAATTTTA
1 TTTTTTAAATTTTA
* *
22280 GTATTTAAATTTTA
1 TTTTTTAAATTTTA
22294 TTTTTTAAA
1 TTTTTTAAA
22303 AATCATTGGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (14 bp):
TTTTTTAAATTTTA
Found at i:29949 original size:29 final size:28
Alignment explanation
Indices: 29895--29950 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
29885 AGGGTGAAAT
*
29895 CTACAGGTCGCCATGCCATCCGGACGAC
1 CTACAGGTCGCCATGCCATCCCGACGAC
* *
29923 CTACTAGGTCGCCATGTCTTCCCGACGA
1 CTAC-AGGTCGCCATGCCATCCCGACGA
29951 GCTATGAGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.20, C:0.38, G:0.23, T:0.20
Consensus pattern (28 bp):
CTACAGGTCGCCATGCCATCCCGACGAC
Found at i:30024 original size:14 final size:14
Alignment explanation
Indices: 30007--30047 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
29997 CATCCGAAGC
30007 CATCCGACCGAGGG
1 CATCCGACCGAGGG
30021 CATCCGACCGAGGG
1 CATCCGACCGAGGG
30035 CATCCGACCGAGG
1 CATCCGACCGAGG
30048 CCATTCGAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.22, C:0.37, G:0.34, T:0.07
Consensus pattern (14 bp):
CATCCGACCGAGGG
Found at i:30060 original size:14 final size:14
Alignment explanation
Indices: 30000--30051 Score: 77
Period size: 14 Copynumber: 3.7 Consensus size: 14
29990 CGTTGGGCAT
*
30000 CCGAAGCCATCCGA
1 CCGAGGCCATCCGA
*
30014 CCGAGGGCATCCGA
1 CCGAGGCCATCCGA
*
30028 CCGAGGGCATCCGA
1 CCGAGGCCATCCGA
30042 CCGAGGCCAT
1 CCGAGGCCAT
30052 TCGAGCGAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.23, C:0.38, G:0.31, T:0.08
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:30060 original size:28 final size:28
Alignment explanation
Indices: 30007--30060 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
29997 CATCCGAAGC
*
30007 CATCCGACCGAGGGCATCCGACCGAGGG
1 CATCCGACCGAGGCCATCCGACCGAGGG
* *
30035 CATCCGACCGAGGCCATTCGAGCGAG
1 CATCCGACCGAGGCCATCCGACCGAG
30061 CTATGCGAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.22, C:0.35, G:0.33, T:0.09
Consensus pattern (28 bp):
CATCCGACCGAGGCCATCCGACCGAGGG
Found at i:30148 original size:29 final size:29
Alignment explanation
Indices: 30107--30212 Score: 203
Period size: 29 Copynumber: 3.7 Consensus size: 29
30097 GAGGAGCAGG
30107 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
30136 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
30165 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
*
30194 CGGAGTGCATGGCGACCTA
1 AGGAGTGCATGGCGACCTA
30213 TGTTGGGAAG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 76 1.00
ACGTcount: A:0.24, C:0.27, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGAGTGCATGGCGACCTACAAGGTCGCC
Found at i:35334 original size:23 final size:23
Alignment explanation
Indices: 35290--35341 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
35280 TAAAATGATC
35290 ATTTGATTTATTTAAATATAAATT
1 ATTT-ATTTATTTAAATATAAATT
* *
35314 TTTTATTTATTTATCAT-TAAATT
1 ATTTATTTATTTA-AATATAAATT
35337 ATTTA
1 ATTTA
35342 ATGAATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
ATTTATTTATTTAAATATAAATT
Found at i:35578 original size:53 final size:53
Alignment explanation
Indices: 35521--35621 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 53
35511 TATATCGTCC
*
35521 GTAAAATGAA-TAACTAATCGAAGAAAATTAAAATTTCAAGGTAGGCACCAATA
1 GTAAAAT-AAGTAACTAATCGAACAAAATTAAAATTTCAAGGTAGGCACCAATA
* ** *
35574 GTAAAATAAGTAATTAATCGAACAAAATTTGAATTTCAAGGTGGGCAC
1 GTAAAATAAGTAACTAATCGAACAAAATTAAAATTTCAAGGTAGGCAC
35622 TTGTCCACCT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 2 0.05
53 40 0.95
ACGTcount: A:0.48, C:0.11, G:0.17, T:0.25
Consensus pattern (53 bp):
GTAAAATAAGTAACTAATCGAACAAAATTAAAATTTCAAGGTAGGCACCAATA
Found at i:36811 original size:22 final size:23
Alignment explanation
Indices: 36770--36812 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
36760 TTCCATTAAA
*
36770 TTTTAAAAATTTAAATTTTATCT
1 TTTTAAAAATTTAAAATTTATCT
36793 TTTTAAAAA-TTAAAATTTAT
1 TTTTAAAAATTTAAAATTTAT
36813 TCCTTAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTAAAAATTTAAAATTTATCT
Found at i:37529 original size:60 final size:60
Alignment explanation
Indices: 37452--37585 Score: 173
Period size: 60 Copynumber: 2.2 Consensus size: 60
37442 TTGGGTCATT
* * ** *
37452 GTTTGAGGACGAATTTAGAATGTTCAAAAGTCTATGGA-CTAATTTAGAATGATGCTCGTA
1 GTTTGAGGATGAATTTAGAATATTCAAAAGTCTAAAGATC-AATTTAGAATGAAGCTCGTA
* *
37512 GTTTG-GGAATGAATTTAGAATATTCAAAAGTTTAAAGATCAATTTAGAATGAAGGTCGTA
1 GTTTGAGG-ATGAATTTAGAATATTCAAAAGTCTAAAGATCAATTTAGAATGAAGCTCGTA
37572 GTTTGAGGATGAAT
1 GTTTGAGGATGAAT
37586 AGTGCAATTA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
59 2 0.03
60 59 0.92
61 3 0.05
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.34
Consensus pattern (60 bp):
GTTTGAGGATGAATTTAGAATATTCAAAAGTCTAAAGATCAATTTAGAATGAAGCTCGTA
Found at i:40874 original size:14 final size:14
Alignment explanation
Indices: 40852--40885 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
40842 CGTTGGGCAT
*
40852 CCGAAGGCATCCGA
1 CCGAGGGCATCCGA
40866 CCGAGGGCATCCGA
1 CCGAGGGCATCCGA
40880 CCGAGG
1 CCGAGG
40886 CCATTCGAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.35, G:0.35, T:0.06
Consensus pattern (14 bp):
CCGAGGGCATCCGA
Found at i:40898 original size:14 final size:14
Alignment explanation
Indices: 40859--40889 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
40849 CATCCGAAGG
*
40859 CATCCGACCGAGGG
1 CATCCGACCGAGGC
40873 CATCCGACCGAGGC
1 CATCCGACCGAGGC
40887 CAT
1 CAT
40890 TCGAGCGAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.39, G:0.29, T:0.10
Consensus pattern (14 bp):
CATCCGACCGAGGC
Found at i:46691 original size:22 final size:22
Alignment explanation
Indices: 46666--46709 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
46656 CATGTAAAAA
*
46666 ATTATATG-CATTATATAATAAT
1 ATTATATGACA-TAAATAATAAT
46688 ATTATATGACATAAATAATAAT
1 ATTATATGACATAAATAATAAT
46710 TATTGTTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (22 bp):
ATTATATGACATAAATAATAAT
Found at i:50831 original size:6 final size:6
Alignment explanation
Indices: 50822--50860 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
50812 GATCATGATG
* * *
50822 ATGGAC ATGGTC ATGGTC ATGGGC ATGGGC ATGGGC ATG
1 ATGGGC ATGGGC ATGGGC ATGGGC ATGGGC ATGGGC ATG
50861 ATGATGATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.21, C:0.15, G:0.41, T:0.23
Consensus pattern (6 bp):
ATGGGC
Found at i:52223 original size:21 final size:21
Alignment explanation
Indices: 52208--52272 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
52198 TAGTTTACGA
52208 TGTTGACATGACAGTTCAAGG
1 TGTTGACATGACAGTTCAAGG
*
52229 TGTTGATATGACAGTTCAAGG
1 TGTTGACATGACAGTTCAAGG
*
52250 TGTTGACATGACAGTTCAGGG
1 TGTTGACATGACAGTTCAAGG
52271 TG
1 TG
52273 ACAGATTAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.26, C:0.12, G:0.31, T:0.31
Consensus pattern (21 bp):
TGTTGACATGACAGTTCAAGG
Found at i:58043 original size:31 final size:31
Alignment explanation
Indices: 57984--58043 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
57974 GGTAGAGTGG
*
57984 CCATTTTGATACAAATCGATAACGTTAGTTA
1 CCATTTTGATACAAATCGATAACATTAGTTA
* *
58015 CCATTTTGTTACAAATCGATAATATTAGT
1 CCATTTTGATACAAATCGATAACATTAGT
58044 GACTAATTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (31 bp):
CCATTTTGATACAAATCGATAACATTAGTTA
Found at i:58054 original size:31 final size:31
Alignment explanation
Indices: 57979--58055 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
57969 ATAATGGTAG
* * * *
57979 AGTGGCCATTTTGATACAAATCGATAACGTT
1 AGTGACCAATTTGTTACAAATCGATAACATT
* * *
58010 AGTTACCATTTTGTTACAAATCGATAATATT
1 AGTGACCAATTTGTTACAAATCGATAACATT
*
58041 AGTGACTAATTTGTT
1 AGTGACCAATTTGTT
58056 TCTTTTAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (31 bp):
AGTGACCAATTTGTTACAAATCGATAACATT
Found at i:59318 original size:2 final size:2
Alignment explanation
Indices: 59267--59299 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
59257 ACCATATGCA
59267 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59300 CATTTTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59508 original size:23 final size:24
Alignment explanation
Indices: 59465--59511 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
59455 ATTACAACAT
59465 AAAATCAATTTAGTTCAAGTTGAAA
1 AAAATCAATTTA-TTCAAGTTGAAA
*
59490 AAAATCAATTT-TTCGAGTTGAA
1 AAAATCAATTTATTCAAGTTGAA
59512 TTGATTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
25 11 0.52
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.34
Consensus pattern (24 bp):
AAAATCAATTTATTCAAGTTGAAA
Found at i:61674 original size:60 final size:60
Alignment explanation
Indices: 61580--61710 Score: 151
Period size: 60 Copynumber: 2.2 Consensus size: 60
61570 TTATTAGCAT
* * *
61580 AAAGTATAC-AAATGGTCCCCTTACTATAAGGTATTATTTTATT-AAGTCTCTCAACTATTA
1 AAAGT-TACAAAATGATCCCCTCACTATAAGGTATTATTTTATTGAA-TCACTCAACTATTA
* * * *
61640 AAAGTTACAAAATGATCCTCTCACTAT-AGAGTATTGTTTTGTTGAATCACTCAACTGTTA
1 AAAGTTACAAAATGATCCCCTCACTATAAG-GTATTATTTTATTGAATCACTCAACTATTA
61700 AAAGTTACAAA
1 AAAGTTACAAA
61711 TTTGGTCACT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
59 5 0.08
60 54 0.89
61 2 0.03
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (60 bp):
AAAGTTACAAAATGATCCCCTCACTATAAGGTATTATTTTATTGAATCACTCAACTATTA
Found at i:63968 original size:2 final size:2
Alignment explanation
Indices: 63961--63992 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
63951 ATAGAATGAC
63961 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63993 TAATTAAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67234 original size:84 final size:84
Alignment explanation
Indices: 67118--67315 Score: 263
Period size: 84 Copynumber: 2.4 Consensus size: 84
67108 ACAGGGGATG
* *
67118 CATTTTTCCATTATTATTCAGAGAAACTCTGGATTATAATAGTGATCCATCATATCCGAAATGAA
1 CATTTTTCCATTATTATTCAGAGAATCTCTGGATTATAATAGTGATCCATCACATCCGAAATGAA
*
67183 AGATGCATTCCAGGAGAAA
66 AGATACATTCCAGGAGAAA
* ** *
67202 CATTTTTCCATTATTATTAAGAGAATCTCTGGATTATAATAGTGATTTATCCCATCCGAAATGAA
1 CATTTTTCCATTATTATTCAGAGAATCTCTGGATTATAATAGTGATCCATCACATCCGAAATGAA
* ** *
67267 AGATACGTTTTAGGAGAAT
66 AGATACATTCCAGGAGAAA
* * *
67286 C-GTTATCCATTATTATTCAGAAAATCTCTG
1 CATTTTTCCATTATTATTCAGAGAATCTCTG
67316 TCATGTCAGA
Statistics
Matches: 99, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
83 25 0.25
84 74 0.75
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (84 bp):
CATTTTTCCATTATTATTCAGAGAATCTCTGGATTATAATAGTGATCCATCACATCCGAAATGAA
AGATACATTCCAGGAGAAA
Found at i:67337 original size:83 final size:82
Alignment explanation
Indices: 67121--67644 Score: 372
Period size: 83 Copynumber: 6.3 Consensus size: 82
67111 GGGGATGCAT
* * * * * * * **
67121 TTTTCCATTATTATTCAGAGAAACTCTG-GATTATAATAGTGATCCATCATATCCGAAATGAAAG
1 TTTTCCATTATTATTCAGAGAATCTCTGTCA-TGTCAGAGTGTTTCATCCCATCCGAAATGAAAG
**
67185 ATGCATTCCAGGAGAAACAT-
65 ATGCATTTTAGGAG--A-ATG
* * * * *
67205 TTTTCCATTATTATTAAGAGAATCTCTG-GATTATAATAGTGATTT-ATCCCATCCGAAATGAAA
1 TTTTCCATTATTATTCAGAGAATCTCTGTCA-TGTCAGAGTG-TTTCATCCCATCCGAAATGAAA
* *
67268 GATACGTTTTAGGAGAATCG
64 GATGCATTTTAGGAGAAT-G
* * * *
67288 TTATCCATTATTATTCAGAAAATCTCTGTCATGTCAGAGTGTTTCATCCCATCCAAAATGAAAGC
1 TTTTCCATTATTATTCAGAGAATCTCTGTCATGTCAGAGTGTTTCATCCCATCCGAAATGAAAGA
* * *
67353 CGCATTTT-GGGGAAAGTA
66 TGCATTTTAGGAG-AA-TG
* * * * *
67371 TTTTCTATTATTAATTCAGAGAATCTTTATCATGTCAGAGT-ATTCAATCCCATTCGAAATG-AA
1 TTTTCCATTATT-ATTCAGAGAATCTCTGTCATGTCAGAGTGTTTC-ATCCCATCCGAAATGAAA
** *
67434 -ATGCGTATTTCGGGGAAAATG
64 GATGC--ATTT-TAGGAGAATG
* * * *
67455 TTTTCCATTATTATTTAGAGAATCTCTGTCAAGTCAGAGTGTTAT-ACCCCATCTGAAATGAAAG
1 TTTTCCATTATTATTCAGAGAATCTCTGTCATGTCAGAGTGTT-TCATCCCATCCGAAATGAAAG
*
67519 GTGCATTTTGAGGA-AAGTG
65 ATGCATTTT-AGGAGAA-TG
* * ** *
67538 TTTTCCATTATTA---AGAGAATCTCTGCCATGTCAGAGTGTTCCATCATATCCGAAACGAAAGA
1 TTTTCCATTATTATTCAGAGAATCTCTGTCATGTCAGAGTGTTTCATCCCATCCGAAATGAAAGA
* *
67600 TGCATTTCGAGGAAAATG
66 TGCATTT-TAGGAGAATG
* *
67618 TTTTCCTTTATTATTTAGAGAATCTCT
1 TTTTCCATTATTATTCAGAGAATCTCT
67645 TCCACTTCAC
Statistics
Matches: 354, Mismatches: 61, Indels: 51
0.76 0.13 0.11
Matches are distributed among these distances:
80 64 0.18
81 4 0.01
82 11 0.03
83 141 0.40
84 125 0.35
85 7 0.02
86 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (82 bp):
TTTTCCATTATTATTCAGAGAATCTCTGTCATGTCAGAGTGTTTCATCCCATCCGAAATGAAAGA
TGCATTTTAGGAGAATG
Found at i:67644 original size:163 final size:165
Alignment explanation
Indices: 67254--67644 Score: 443
Period size: 167 Copynumber: 2.4 Consensus size: 165
67244 TGATTTATCC
* * * * * * *
67254 CATCCGAAATGAAAGATACGTTT-TAGGAGAATCGTTATCCATTATTATTCAGAAAATCTCTGTC
1 CATCCGAAATGAAAGATGCATTTCGAGGAAAAT-GTTTTCCATTATTATTTAGAGAATCTCTGTC
* * * *
67318 ATGTCAGAGTGTTTCATCCCATCCAAAATGAAAGCCGCATTTTGGGGAAAGTATTTTCTATTATT
65 AAGTCAGAGTGTTTCACCCCATCCAAAATGAAAGCCGCATTTTGAGGAAAGTATTTTCCATTATT
* * *
67383 AATTCAGAGAATCTTTATCATGTCAGAGTATTCAATCC
130 AA-T-AGAGAATCTCTACCATGTCAGAGTATTCAATCA
* *
67421 CATTCGAAATG-AA-ATGCGTATTTCGGGGAAAATGTTTTCCATTATTATTTAGAGAATCTCTGT
1 CATCCGAAATGAAAGATGC--ATTTCGAGGAAAATGTTTTCCATTATTATTTAGAGAATCTCTGT
** ** *
67484 CAAGTCAGAGTGTTAT-ACCCCATCTGAAATGAAAGGTGCATTTTGAGGAAAGTGTTTTCCATTA
64 CAAGTCAGAGTGTT-TCACCCCATCCAAAATGAAAGCCGCATTTTGAGGAAAGTATTTTCCATTA
* * *
67548 TT-A-AGAGAATCTCTGCCATGTCAGAGTGTTCCATCA
128 TTAATAGAGAATCTCTACCATGTCAGAGTATTCAATCA
* * *
67584 TATCCGAAACGAAAGATGCATTTCGAGGAAAATGTTTTCCTTTATTATTTAGAGAATCTCT
1 CATCCGAAATGAAAGATGCATTTCGAGGAAAATGTTTTCCATTATTATTTAGAGAATCTCT
67645 TCCACTTCAC
Statistics
Matches: 189, Mismatches: 29, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
163 75 0.40
164 2 0.01
165 7 0.04
166 3 0.02
167 95 0.50
168 7 0.04
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Consensus pattern (165 bp):
CATCCGAAATGAAAGATGCATTTCGAGGAAAATGTTTTCCATTATTATTTAGAGAATCTCTGTCA
AGTCAGAGTGTTTCACCCCATCCAAAATGAAAGCCGCATTTTGAGGAAAGTATTTTCCATTATTA
ATAGAGAATCTCTACCATGTCAGAGTATTCAATCA
Found at i:70089 original size:22 final size:22
Alignment explanation
Indices: 70061--70105 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
70051 GATTAGTAGC
*
70061 AGATTTGTAACAAAATGTTACA
1 AGATTTGTAACAAAAGGTTACA
70083 AGATTTGTAACAAAAGGTTACA
1 AGATTTGTAACAAAAGGTTACA
70105 A
1 A
70106 CATCAAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.29
Consensus pattern (22 bp):
AGATTTGTAACAAAAGGTTACA
Found at i:73908 original size:28 final size:28
Alignment explanation
Indices: 73877--73944 Score: 136
Period size: 28 Copynumber: 2.4 Consensus size: 28
73867 ATCTAGTTAT
73877 TGAGGTTTCTTGTATATCTGGGTCATAA
1 TGAGGTTTCTTGTATATCTGGGTCATAA
73905 TGAGGTTTCTTGTATATCTGGGTCATAA
1 TGAGGTTTCTTGTATATCTGGGTCATAA
73933 TGAGGTTTCTTG
1 TGAGGTTTCTTG
73945 CTGTTGTGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.19, C:0.10, G:0.26, T:0.44
Consensus pattern (28 bp):
TGAGGTTTCTTGTATATCTGGGTCATAA
Found at i:77338 original size:15 final size:15
Alignment explanation
Indices: 77318--77348 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
77308 AAGGAGAGAA
77318 CCTCCGTTCAGACAG
1 CCTCCGTTCAGACAG
77333 CCTCCGTTCAGACAG
1 CCTCCGTTCAGACAG
77348 C
1 C
77349 GGAAAGCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.42, G:0.19, T:0.19
Consensus pattern (15 bp):
CCTCCGTTCAGACAG
Done.